X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=7351ff415ec13f7d919f8bd970e62c2d3fbac398;hb=98aabcd507dd44fa7d2c8dc7dbfccb346eae84a3;hp=1df0a70cefa43f0ddacee098d1842d297c3f18af;hpb=80fc4809a35964d96c9b1e824db42288dc406a27;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 1df0a70c..7351ff41 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/02/10 09:07:19 $ - Version: $Revision: 1.219 $ + Date: $Date: 2005/03/22 11:37:15 $ + Version: $Revision: 1.231 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -46,12 +46,25 @@ namespace gdcm { //----------------------------------------------------------------------------- // Constructor / Destructor + +/** + * \brief Constructor used when we want to generate dicom files from scratch + */ +File::File(): + Document() +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + GrPixel = 0x7fe0; + NumPixel = 0x0010; +} + /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ File::File( std::string const &filename ) - :Document( filename ) + :Document(filename) { RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; @@ -115,7 +128,6 @@ File::File( std::string const &filename ) // Create a new BinEntry to change the the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) - // - a VM to "PXL" // - the name to "Pixel Data" BinEntry *oldEntry = dynamic_cast(entry); if(oldEntry) @@ -146,16 +158,6 @@ File::File( std::string const &filename ) } } -/** - * \brief Constructor used when we want to generate dicom files from scratch - */ -File::File(): - Document() -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - InitializeDefaultFile(); -} /** * \brief Canonical destructor. @@ -170,6 +172,8 @@ File::~File () //----------------------------------------------------------------------------- // Public + + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -216,13 +220,7 @@ bool File::IsReadable() */ int File::GetImageNumber() { - // The function i atoi() takes the address of an area of memory as - // parameter and converts the string stored at that location to an integer - // using the external decimal to internal binary conversion rules. This may - // be preferable to sscanf() since atoi() is a much smaller, simpler and - // faster function. sscanf() can do all possible conversions whereas - // atoi() can only do single decimal integer conversions. - //0020 0013 IS REL Image Number + //0020 0013 : Image Number std::string strImNumber = GetEntryValue(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { @@ -237,7 +235,7 @@ int File::GetImageNumber() */ ModalityType File::GetModality() { - // 0008 0060 CS ID Modality + // 0008 0060 : Modality std::string strModality = GetEntryValue(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { @@ -270,10 +268,14 @@ ModalityType File::GetModality() else if ( strModality.find("PT") < strModality.length()) return PT; else if ( strModality.find("RF") < strModality.length()) return RF; else if ( strModality.find("RG") < strModality.length()) return RG; - else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; - else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; - else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; - else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; + else if ( strModality.find("RTDOSE") + < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") + < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") + < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") + < strModality.length()) return RTSTRUCT; else if ( strModality.find("SM") < strModality.length()) return SM; else if ( strModality.find("ST") < strModality.length()) return ST; else if ( strModality.find("TG") < strModality.length()) return TG; @@ -367,7 +369,8 @@ int File::GetZSize() */ float File::GetXSpacing() { - float xspacing, yspacing; + float xspacing = 1.0; + float yspacing = 1.0; const std::string &strSpacing = GetEntryValue(0x0028,0x0030); if( strSpacing == GDCM_UNFOUND ) @@ -400,7 +403,7 @@ float File::GetXSpacing() if ( xspacing == 0.) { - gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); + gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem"); // seems to be a bug in the header ... nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); gdcmAssertMacro( nbValues == 2 ); @@ -446,15 +449,15 @@ float File::GetYSpacing() */ float File::GetZSpacing() { - // Spacing Between Slices : distance entre le milieu de chaque coupe - // Les coupes peuvent etre : + // Spacing Between Slices : distance between the middle of 2 slices + // Slices may be : // jointives (Spacing between Slices = Slice Thickness) - // chevauchantes (Spacing between Slices < Slice Thickness) + // overlapping (Spacing between Slices < Slice Thickness) // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal - // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... - // Si le Spacing Between Slices est Missing, - // on suppose que les coupes sont jointives + // It only concerns the MRI guys, not people wanting to visualize volmues + // If Spacing Between Slices is Missing, + // we suppose slices joint together const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); @@ -778,7 +781,7 @@ int File::GetPixelSize() * - 32S signed 32 bit, * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. - * 24 bit images appear as 8 bit + * 24 bit images appear as 8 bit + photochromatic interp ="RGB " * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() @@ -846,8 +849,8 @@ bool File::IsSignedPixelData() } /** - * \brief Check whether this a monochrome picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * \brief Check whether this a monochrome picture (gray levels) or not, + * using "Photometric Interpretation" tag (0x0028,0x0004). * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ bool File::IsMonochrome() @@ -865,6 +868,25 @@ bool File::IsMonochrome() return false; } +/** + * \brief Check whether this a MONOCHROME1 picture (high values = dark) + * or not using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" . False otherwise. + */ +bool File::IsMonochrome1() +{ + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; +} + /** * \brief Check whether this a "PALETTE COLOR" picture or not by accessing * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). @@ -1158,21 +1180,17 @@ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, void File::AnonymizeNoLoad() { std::fstream *fp = new std::fstream(Filename.c_str(), - std::ios::in | std::ios::out | std::ios::binary); - - // TODO : FIXME - // how to white out disk space if longer than 50 ? - char spaces[50] = " "; - + std::ios::in | std::ios::out | std::ios::binary); gdcm::DocEntry *d; uint32_t offset; uint32_t lgth; - uint32_t lgtToWrite; + uint32_t valLgth = 0; + std::string *spaces; for (ListElements::iterator it = AnonymizeList.begin(); it != AnonymizeList.end(); ++it) { - d = GetDocEntry( (*it).Group, (*it).Elem); + d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) continue; @@ -1181,30 +1199,17 @@ void File::AnonymizeNoLoad() || dynamic_cast(d) ) continue; - if( d == NULL) - { - gdcmWarningMacro( "I have no idea why this is NULL " - << "but this solves the seg fault"); - continue; - } offset = d->GetOffset(); lgth = d->GetLength(); - fp->seekp( offset, std::ios::beg ); - - if ( (*it).Value == "" ) + if (valLgth < lgth) { - lgtToWrite = lgth > 50 ? 50 : lgth; - fp->write( spaces, lgtToWrite ); - } - else - { - // TODO : FIXME - // how to white out disk space if longer than 50 ? - (*it).Value = (*it).Value + spaces; - lgtToWrite = lgth > (*it).Value.length() ? (*it).Value.length() : lgth; - fp->write( (char *)(*it).Value.c_str(), lgtToWrite ); - + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + } fp->close(); delete fp; @@ -1216,7 +1221,7 @@ void File::AnonymizeNoLoad() */ bool File::AnonymizeFile() { - // If Anonymisation list is empty, let's perform some basic anonymisation + // If Anonymisation list is empty, let's perform some basic anonymization if ( AnonymizeList.begin() == AnonymizeList.end() ) { // If exist, replace by spaces @@ -1255,12 +1260,6 @@ bool File::AnonymizeFile() || dynamic_cast(d) ) continue; - if( d == NULL) - { - gdcmWarningMacro( "I have no idea why this is NULL " - << "but this solves the seg fault"); - continue; - } SetValEntry ((*it).Value, (*it).Group, (*it).Elem); } } @@ -1325,10 +1324,10 @@ bool File::AnonymizeFile() * (as opposed to 'DicomDir related') entries * then writes in a file all the (Dicom Elements) included the Pixels * @param fileName file name to write to - * @param filetype Type of the File to be written + * @param writetype Type of the File to be written * (ACR, ExplicitVR, ImplicitVR) */ -bool File::Write(std::string fileName, FileType filetype) +bool File::Write(std::string fileName, FileType writetype) { std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); @@ -1339,12 +1338,12 @@ bool File::Write(std::string fileName, FileType filetype) } // Entry : 0002|0000 = group length -> recalculated - ValEntry *e0002 = GetValEntry(0x0002,0x0000); - if( e0002 ) + ValEntry*e0000 = GetValEntry(0x0002,0x0000); + if( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(filetype); - e0002->SetValue(sLen.str()); + sLen << ComputeGroup0002Length(writetype); + e0000->SetValue(sLen.str()); } // Bits Allocated @@ -1404,7 +1403,7 @@ bool File::Write(std::string fileName, FileType filetype) } } - Document::WriteContent(fp, filetype); + Document::WriteContent(fp, writetype); fp->close(); delete fp; @@ -1414,90 +1413,7 @@ bool File::Write(std::string fileName, FileType filetype) //----------------------------------------------------------------------------- // Protected -/** - * \brief Initialize a default DICOM File that should contain all the - * field require by other reader. DICOM standard does not - * explicitely defines those fields, heuristic has been choosen. - * This is not perfect as we are writting a CT image... - */ -void File::InitializeDefaultFile() -{ - std::string date = Util::GetCurrentDate(); - std::string time = Util::GetCurrentTime(); - std::string uid = Util::CreateUniqueUID(); - std::string uidMedia = uid; - std::string uidInst = uid; - std::string uidClass = Util::CreateUniqueUID(); - std::string uidStudy = Util::CreateUniqueUID(); - std::string uidSerie = Util::CreateUniqueUID(); - - // Meta Element Group Length - InsertValEntry("146 ", 0x0002, 0x0000); - // Media Storage SOP Class UID (CT Image Storage) - InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002); - // Media Storage SOP Instance UID - InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003); - // Transfer Syntax UID (Explicit VR Little Endian) - InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010); - // META Implementation Class UID - InsertValEntry(uidClass.c_str(), 0x0002, 0x0012); - // Source Application Entity Title - InsertValEntry("GDCM", 0x0002, 0x0016); - - // Instance Creation Date - InsertValEntry(date.c_str(), 0x0008, 0x0012); - // Instance Creation Time - InsertValEntry(time.c_str(), 0x0008, 0x0013); - // SOP Class UID - InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016); - // SOP Instance UID - InsertValEntry(uidInst.c_str(), 0x0008, 0x0018); - // Modality - InsertValEntry("CT", 0x0008, 0x0060); - // Manufacturer - InsertValEntry("GDCM", 0x0008, 0x0070); - // Institution Name - InsertValEntry("GDCM", 0x0008, 0x0080); - // Institution Address - InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081); - - // Patient's Name - InsertValEntry("GDCM", 0x0010, 0x0010); - // Patient ID - InsertValEntry("GDCMID", 0x0010, 0x0020); - - // Study Instance UID - InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d); - // Series Instance UID - InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e); - // StudyID - InsertValEntry("1", 0x0020, 0x0010); - // SeriesNumber - InsertValEntry("1", 0x0020, 0x0011); - - // Samples per pixel 1 or 3 - InsertValEntry("1", 0x0028, 0x0002); - // photochromatic interpretation - InsertValEntry("MONOCHROME1", 0x0028, 0x0004); - // nbRows - InsertValEntry("0", 0x0028, 0x0010); - // nbCols - InsertValEntry("0", 0x0028, 0x0011); - // BitsAllocated 8 or 12 or 16 - InsertValEntry("8", 0x0028, 0x0100); - // BitsStored <= BitsAllocated - InsertValEntry("8", 0x0028, 0x0101); - // HighBit <= BitsAllocated - 1 - InsertValEntry("7", 0x0028, 0x0102); - // Pixel Representation 0(unsigned) or 1(signed) - InsertValEntry("0", 0x0028, 0x0103); - - // default value - // Special case this is the image (not a string) - GrPixel = 0x7fe0; - NumPixel = 0x0010; - InsertBinEntry(0, 0, GrPixel, NumPixel); -} + //----------------------------------------------------------------------------- // Private